ObjectiveTo systematically review the effect of oral intake of bacterial probiotics on 15 variables related to obesity, diabetes and non-alcoholic fatty liver disease.DesignSystematic review and meta-analysis.Data sourcesMedline, EMBASE and COCHRANE from 1990 to June 2018.Eligibility criteriaRandomised controlled trials (≥14 days) excluding hypercholesterolaemia, alcoholic liver disease, polycystic ovary syndrome and children <3 years.ResultsOne hundred and five articles met inclusion criteria, representing 6826 subjects. In overweight but not obese subjects, probiotics induced improvements in: body weight (k=25 trials, d=−0.94 kg mean difference, 95% CI −1.17 to −0.70, I²=0.0%), body mass index (k=32, d=−0.55 kg/m², 95% CI −0.86 to −0.23, I²=91.9%), waist circumference (k=13, d=−1.31 cm, 95% CI −1.79 to −0.83, I²=14.5%), body fat mass (k=11, d=−0.96 kg, 95% CI −1.21 to −0.71, I²=0.0%) and visceral adipose tissue mass (k=5, d=−6.30 cm², 95% CI −9.05 to −3.56, I²=0.0%). In type 2 diabetics, probiotics reduced fasting glucose (k=19, d=−0.66 mmol/L, 95% CI −1.00 to −0.31, I²=27.7%), glycated haemoglobin (k=13, d=−0.28 pp, 95% CI −0.46 to −0.11, I²=54.1%), insulin (k=13, d=−1.66 mU/L, 95% CI −2.70 to −0.61, I²=37.8%) and homeostatic model of insulin resistance (k=10, d=−1.05 pp, 95% CI −1.48 to −0.61, I²=18.2%). In subjects with fatty liver diseases, probiotics reduced alanine (k=12, d=−10.2 U/L, 95% CI −14.3 to −6.0, I²=93.50%) and aspartate aminotransferases (k=10, d=−9.9 U/L, 95% CI −14.1 to -5.8, I²=96.1%). These improvements were mostly observed with bifidobacteria (Bifidobacterium breve, B. longum), Streptococcus salivarius subsp. thermophilus and lactobacilli (Lactobacillus acidophilus, L. casei, L. delbrueckii) containing mixtures and influenced by trials conducted in one country.ConclusionsThe intake of probiotics resulted in minor but consistent improvements in several metabolic risk factors in subjects with metabolic diseases.Trial registration numberCRD42016033273.